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A few more class docstrings, removed excess blank lines

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1 parent d694e10 commit df42f53bf27f016ed14d8ecfb051c419ba58d7d3 @peterjc peterjc committed Mar 21, 2013
Showing with 7 additions and 8 deletions.
  1. +7 −8 Bio/Alphabet/__init__.py
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@@ -12,8 +12,7 @@
class Alphabet(object):
-
- """Generic unspecified alphabet.
+ """Generic alphabet base class.
This class is used as a base class for other types of alphabets.
@@ -82,9 +81,7 @@ def _lower(self):
class SingleLetterAlphabet(Alphabet):
-
- """Generic alphabet with letters of size 1."""
-
+ """Generic alphabet with letters of size one."""
size = 1
letters = None # string of all letters in the alphabet
@@ -94,6 +91,7 @@ class SingleLetterAlphabet(Alphabet):
class ProteinAlphabet(SingleLetterAlphabet):
+ """Generic single letter protein alphabet."""
pass
generic_protein = ProteinAlphabet()
@@ -102,12 +100,14 @@ class ProteinAlphabet(SingleLetterAlphabet):
class NucleotideAlphabet(SingleLetterAlphabet):
+ """Generic single letter nucleotide alphabet."""
pass
generic_nucleotide = NucleotideAlphabet()
class DNAAlphabet(NucleotideAlphabet):
+ """Generic single letter DNA alphabet."""
pass
generic_dna = DNAAlphabet()
@@ -117,6 +117,7 @@ class DNAAlphabet(NucleotideAlphabet):
class RNAAlphabet(NucleotideAlphabet):
+ """Generic single letter RNA alphabet."""
pass
generic_rna = RNAAlphabet()
@@ -125,17 +126,15 @@ class RNAAlphabet(NucleotideAlphabet):
class SecondaryStructure(SingleLetterAlphabet):
-
"""Alphabet used to describe secondary structure.
Letters are 'H' (helix), 'S' (strand), 'T' (turn) and 'C' (coil).
-
"""
-
letters = "HSTC"
class ThreeLetterProtein(Alphabet):
+ """Three letter protein alphabet."""
size = 3
letters = [
"Ala", "Asx", "Cys", "Asp", "Glu", "Phe", "Gly", "His", "Ile",

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